[Chimera-users] Mirror image proteins

[Eric Pettersen]

Hi Nancy,
	The script assumes you only have one model open and flips that model in its entirety.  Here’s a slightly tweaked version that flips all open molecular models:

from chimera import openModels, Molecule
for m in openModels.list(modelTypes=[Molecule]):
	for a in m.atoms:
		crd = a.coord()
		crd.x = 0 - crd.x
		a.setCoord(crd)

You don’t have to type it into the IDLE shell.  Instead, you could save the above into a file whose name ends in ‘.py’ (indicating it’s a Python file).  The you could run the script simply by opening it in Chimera with File→Open or the “open” command.
	I don’t know what you read on GitHub, but if you really need to restrict the script to working on a model with a particular ID#, it’s possible to make the script do that.  Let me know if that’s what you need.
	It would be weird to flip just part of a model.  Consider a model with two chains where the Z coordinate of all the atoms are in the range 30-40.  Flipping the Z coordinate of one of the chains would move it far away from the other chain.

—Eric


	Eric Pettersen
	UCSF Computer Graphics Lab




> On Sep 1, 2018, at 8:32 AM, Chu Ji <nancyji0217 at gmail.com> wrote:
> 
> Hi Eric,
>  
> I was trying to get a mirror image of a PDB model and came across your thread. I know that you are typing in 
> m = chimera.openModels.list()[0]
> for a in m.atoms:
>     crd = a.coord()
>     crd.z = 0 - crd.z
>     a.setCoord(crd)
> in the Gen Control>IDLE section, but I also read on GitHub that I should change the [0] in openModels.list()[0]to the model specifier. What does that mean exactly? I tried to type in the PDB ID to replace the 0 but nothing happened…Could you show me an example? What if I want to flip Chain B of a certain model or just the entire model?
>  
> Thank you so much for your help! Looking forward to hearing from you.
>  
> Best,
> Nancy
>  
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>  
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